For RNAP2 ChIP, chromatin isolated from fixed nuclei was sonicated and incubated at 4ºC overnight with either Protein A Dynabeads (Invitrogen) coated with rabbit anti-RNAP2 antibody. Single-end high throughput sequencing libraries were prepared from 10ng of ChIP DNA using NEB Ultra DNA Library Prep kit for Illumina, and sequenced according to the manufacturer's protocols using Illumina Hi-seq2500. For MNase-seq, chromatin from fixed nuclei was digested with MNase and DNA was purified after digestion. Paired-end high throughput sequencing libraries were prepared from 50ng of digested DNA using NEB Ultra DNA Library Prep kit for Illumina, without size selection steps, and sequenced according to the manufacturer's protocols using Illumina Hi-seq2500.